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Biomarkers in T-cell therapy clinical trials. Cytotherapy 2013; 15:632-40. [DOI: 10.1016/j.jcyt.2013.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 01/01/2013] [Indexed: 01/13/2023]
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Gill S, Kalos M. T cell-based gene therapy of cancer. Transl Res 2013; 161:365-79. [PMID: 23246626 DOI: 10.1016/j.trsl.2012.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/15/2012] [Accepted: 11/16/2012] [Indexed: 01/20/2023]
Abstract
Adoptive immunotherapy using gene engineered T cells is a promising and rapidly evolving field, and the ability to engineer T cells to manifest desired phenotypes and functions has become a practical reality. In this review, we describe and summarize current thought about gene engineering of T cells. We focus on the identified requirements for the successful application of T cell based immunotherapy and discuss gene-therapy based strategies that address these requirements and have the potential to enhance the successful implementation of this promising approach to treat cancer.
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Affiliation(s)
- Saar Gill
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa., USA
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Kalos M. Biomarkers in T cell therapy clinical trials. J Transl Med 2011; 9:138. [PMID: 21851646 PMCID: PMC3170602 DOI: 10.1186/1479-5876-9-138] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 08/19/2011] [Indexed: 12/01/2022] Open
Abstract
T cell therapy represents an emerging and promising modality for the treatment of both infectious disease and cancer. Data from recent clinical trials have highlighted the potential for this therapeutic modality to effect potent anti-tumor activity. Biomarkers, operationally defined as biological parameters measured from patients that provide information about treatment impact, play a central role in the development of novel therapeutic agents. In the absence of information about primary clinical endpoints, biomarkers can provide critical insights that allow investigators to guide the clinical development of the candidate product. In the context of cell therapy trials, the definition of biomarkers can be extended to include a description of parameters of the cell product that are important for product bioactivity. This review will focus on biomarker studies as they relate to T cell therapy trials, and more specifically: i. An overview and description of categories and classes of biomarkers that are specifically relevant to T cell therapy trials, and ii. Insights into future directions and challenges for the appropriate development of biomarkers to evaluate both product bioactivity and treatment efficacy of T cell therapy trials.
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Affiliation(s)
- Michael Kalos
- Department of Pathology and Laboratory Medicines, University of Pennsylvania Perelman School of Medicine, Abramson Family Cancer Research Institute, 422 Curie Boulevard, Stellar-Chance Laboratories, Philadelphia, PA 19104-4283, USA.
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Bashashati A, Brinkman RR. A survey of flow cytometry data analysis methods. Adv Bioinformatics 2009; 2009:584603. [PMID: 20049163 PMCID: PMC2798157 DOI: 10.1155/2009/584603] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 07/20/2009] [Accepted: 08/22/2009] [Indexed: 02/04/2023] Open
Abstract
Flow cytometry (FCM) is widely used in health research and in treatment for a variety of tasks, such as in the diagnosis and monitoring of leukemia and lymphoma patients, providing the counts of helper-T lymphocytes needed to monitor the course and treatment of HIV infection, the evaluation of peripheral blood hematopoietic stem cell grafts, and many other diseases. In practice, FCM data analysis is performed manually, a process that requires an inordinate amount of time and is error-prone, nonreproducible, nonstandardized, and not open for re-evaluation, making it the most limiting aspect of this technology. This paper reviews state-of-the-art FCM data analysis approaches using a framework introduced to report each of the components in a data analysis pipeline. Current challenges and possible future directions in developing fully automated FCM data analysis tools are also outlined.
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Affiliation(s)
- Ali Bashashati
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3
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Christmas SE, Halliday D, Lawton N, Wang H, Abdalla I, Masters J, Hassan RL, Hart IJ, Khan N, Smith J, Hammad A, Bakran A. Cytomegalovirus-specific CD8+ T cells do not develop in all renal transplant patients at risk of virus infection. Transpl Immunol 2009; 22:99-104. [DOI: 10.1016/j.trim.2009.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 12/30/2022]
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Lim JB, Kim HO, Jeong SH, Ha JE, Jang S, Lee SG, Lee K, Stroncek D. Identification of HLA-A*2402-restricted HCMV immediate early-1 (IE-1) epitopes as targets for CD8+ HCMV-specific cytotoxic T lymphocytes. J Transl Med 2009; 7:72. [PMID: 19698161 PMCID: PMC2739166 DOI: 10.1186/1479-5876-7-72] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 08/23/2009] [Indexed: 11/23/2022] Open
Abstract
Background To identify novel HLA-A*2402-restricted human cytomegalovirus (HCMV) immediate early-1 (IE-1) epitopes for adoptive immunotherapy, we explored 120 overlapping 15-amino acid spanning IE-1. Methods These peptides were screened by measuring the frequency of polyclonal CD8+ T cells producing intracellular interferon-γ (IFN-γ) using flow cytometry and the epitopes were validated with a HCMV-infected target Cr release cytotoxicity assay. Results Initial screening was performed with 12 mini-pools of 10 consecutive peptides made from 120 overlapping peptides15-amino acids in length that spanned IE-1. When peripheral blood mononuclear cells (PBMCs) from HLA-A*2402 HCMV-seropositive donors were sensitized with each of the 12 mini-pools, mini-pools 1 and 2 induced the highest frequency of CD8+ cytotoxic T lymphocytes (CTLs) producing IFN-γ. When PBMCs were stimulated with each of the twenty peptides belonging to mini-pools 1 and 2, peptides IE-11–15MESSAKRKMDPDNPD and IE-15–19AKRKMDPDNPDEGPS induced the greatest quantities of IFN-γ production and cytotoxicity of HLA-matched HCMV-infected fibroblasts. To determine the exact HLA-A*2402-restricted epitopes within the two IE-1 proteins, we synthesized a total of twenty-one overlapping 9- or 10 amino acid peptides spanning IE-11–15 and IE-15–19. Peptide IE-13–12SSAKRKMDPD induced the greatest quantities of IFN-γ production and target cell killing by CD8+ CTLs. Conclusion HCMV IE-13–12SSAKRKMDPD is a HLA-A*2402-restricted HCMV IE-1 epitope that can serve as a common target for CD8+ HCMV-specific CTLs.
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Affiliation(s)
- Jong-Baeck Lim
- Department of Transfusion Medicine, Warren G, Magnuson Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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de Graaf MT, de Beukelaar JW, Burgers PC, Luider TM, Kraan J, Smitt PAS, Gratama JW. Contamination of synthetic HuD protein spanning peptide pools with a CMV-encoded peptide. Cytometry A 2008; 73:1079-85. [PMID: 18727061 DOI: 10.1002/cyto.a.20636] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To detect HuD-specific T cells in patients with Hu-antibody associated paraneoplastic neurological syndromes (Hu-PNS), we used short-term stimulation assays with HuD protein spanning peptide pools (PSPP) with purities of at least 70% and found reproducible false-positive CD8+ T-cell responses in three of 127 individuals (two healthy controls and one Hu-PNS patient), which all shared HLA-A*2402 and HLA-B*1801. After testing the 15-mer peptides of the HuD antigen separately, we discovered that the same three 15-mers yielded the CD8+ T cell response in those three individuals. This highly unusual result could not be reproduced when using new batches of peptides with a higher level of purity (>82% and >95%). Therefore, we assumed this response was not directed against the HuD peptides and analyzed the HuD 15-mers by Fourier transform ion cyclotron resonance (FT-ICR) tandem mass spectrometry (MS/MS), which showed the presence of a cytomegalovirus (CMV)-encoded peptide (AIAEESDEEEAIVAY) as a contaminant. The three responding individuals all were CMV-seropositive and the contaminating peptide appeared to fit in the binding groove of HLA-B*18. Our data reveal that synthetic PSPP may contain immunogenic contaminations which may cause false positive results in T-cell stimulation assays.
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Affiliation(s)
- Marieke T de Graaf
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Nomura L, Maino VC, Maecker HT. Standardization and optimization of multiparameter intracellular cytokine staining. Cytometry A 2008; 73:984-91. [PMID: 18612990 DOI: 10.1002/cyto.a.20602] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Intracellular cytokine staining (ICS) is a common method for rapid quantitation of cytokine-producing antigen-specific T cells. T cell production of IFNgamma in particular, and more recently IL-2 as well, is often taken as a measure of vaccine immunogenicity in experimental vaccine trials. As more fluorochromes become available for use in ICS and other applications detecting intracellular markers, the selection of optimal fluorochrome combinations becomes correspondingly more complicated. Additionally, as more sophisticated flow cytometers become available, more attention is being paid to potential result variability from one instrument to another. This review summarizes an oral presentation given at MASIR 2008, January 30-Feb 1, 2008, in La Plagne, France. We focus on issues associated with multiparameter (>four color) flow cytometry, including matching antibody specificities with available fluorochromes and techniques to optimize fluorochrome combinations. We examine issues specific to intracellular staining as well as broader topics such as instrument setup, experimental controls, sample management, and analysis of multiparameter data sets. Particular emphasis is placed on the use of lyophilized cells, antibodies, beads, peptides, etc. (collectively known as "lyoplates"), which can decrease experiment-to-experiment variability as well as processing time. Most clinical trials compile results from multiple testing sites, using data that was acquired on-site in each location. We present data from two different ongoing multi-laboratory standardization studies, one involving 15 laboratories and one involving nine. We identify issues of variability and, where possible, offer solutions.
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Affiliation(s)
- Laurel Nomura
- BD Biosciences, 2350 Qume Dr., San Jose, California 95131, USA.
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Li Pira G, Ivaldi F, Bottone L, Manca F. High throughput functional microdissection of pathogen-specific T-cell immunity using antigen and lymphocyte arrays. J Immunol Methods 2007; 326:22-32. [PMID: 17673252 DOI: 10.1016/j.jim.2007.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 05/28/2007] [Accepted: 06/22/2007] [Indexed: 11/15/2022]
Abstract
The analysis of the human T-cell response specific for relevant pathogens is useful for diagnostic purposes and for research. Several methods enumerate antigen specific T-cells and measure their functions. Since screening of numerous antigens from pathogens is often needed to evaluate immunocompetence, lymphocytes, labor and cost are limiting factors. To examine pathogen-specific T-cell immunity, we have miniaturized the analysis of T-cell responses using an array approach in 384- and 1536-well plates with as few as 10 x 10(3) PBMC per well instead of the 500 x 10(3) PBMC used for current assays. Secreted cytokines were detected in the same wells used for lymphocyte cultures. The method can detect about ten CMV specific T-cells diluted into 50 x 10(3) PBMC (0.02%), and can quantify secreted cytokines. The microarray approach allowed evaluation of T-cell immunity in children with a sensitivity higher than current methods. When applied to CMV epitope mapping, the data obtained with conventional methods were confirmed. The assay could be automated, allowing high throughput processing. The assay provides quantitative information on cytokines induced by antigen stimulation and can be applied in a simplified format as a field test to monitor T-cell immunity in vaccine trials or in veterinary medicine.
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Affiliation(s)
- Giuseppina Li Pira
- Cellular Immunology Unit, Advanced Biotechnology Center, Largo Benzi 10, 16132 Genoa, Italy.
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Li Pira G, Kern F, Gratama J, Roederer M, Manca F. Measurement of antigen specific immune responses: 2006 update. CYTOMETRY PART B-CLINICAL CYTOMETRY 2007; 72:77-85. [PMID: 17285633 DOI: 10.1002/cyto.b.20186] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Measuring antigen-specific immune responses (MASIR) is essential for basic immunological research and in the clinical setting. Numerous techniques have been used and the recent years have witnessed a flourishing of flow cytometry based methods for the identification of antigen specific T cells, in addition to other methodologies. The second MASIR conference held in Santorini, Greece, from 14 to 18 June 2006 has been a forum for the discussion of methodological issues and for research or clinical applications of these techniques, as reviewed here. In addition to flow cytometry based techniques, other emerging techniques with different degrees of complexity can be applied. These novel methods are highly promising in numerous conditions to look for correlates of protection, to test responses to natural infections or to vaccination trials, to evaluate the immune status of immunocompromised patients and to monitor persistence and function of specific T cells administered as adoptive therapy.
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Affiliation(s)
- Giuseppina Li Pira
- Viral Immunology, Advanced Biotechnology Center, Largo Benzi 10, 16132 Genoa, Italy.
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Avetisyan G, Larsson K, Aschan J, Nilsson C, Hassan M, Ljungman P. Impact on the cytomegalovirus (CMV) viral load by CMV-specific T-cell immunity in recipients of allogeneic stem cell transplantation. Bone Marrow Transplant 2006; 38:687-92. [PMID: 17001346 DOI: 10.1038/sj.bmt.1705507] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Patients experience cytomegalovirus (CMV) reactivation after stem cell transplantation (SCT) and need repeated courses of pre-emptive therapy. Analysis of CMV-specific immunity might help to assess the need for antiviral therapy. Forty-eight patients were studied during the first 3 months after SCT. Peripheral blood lymphocytes were stimulated by CMV antigen, and interferon (INF)-gamma production by CD3+ and CD4+ T cells was analysed. Results were correlated to transplant factors and CMV disease. Patients with INF-gamma production by CD3+ cells at 4 weeks after SCT had lower peak viral loads than patients with no such production (P=0.03). There was a similar tendency as regards CD4+ cells (P=0.09). Patients who underwent reduced-intensity conditioning (RIC) more frequently had CD3+ (48%) and CD4+ immunity (56%) 4 weeks after SCT compared with patients who received myeloablative conditioning (CD3+ 25%; CD4+ 35%). There was no effect of stem cell source, donor type or acute graft-versus-host disease. Three of 48 patients developed CMV disease and none of them had detectable INF-gamma production. CMV-specific T-cell response is associated with a lower rate of CMV replication. RIC results in improved T-cell reconstitution. Recovery of CMV-specific immunity might be delayed in patients with CMV disease. These observations suggest that detection of CMV-specific T-cells is useful in assessing the immunity against CMV.
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Affiliation(s)
- G Avetisyan
- Department of Medicine, Division of Haematology, Karolinska Institutet, Karolinska University Hospital in Huddinge, Stockholm 14186, Sweden.
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Buxbaum S, Kraus FB, Hahn A, Beck O, Kabartas B, Doerr HW, Ludwig B. Flow cytometric analysis of virus-specific T lymphocytes: Practicability of detection of HCMV-specific T lymphocytes in whole blood in patients after stem cell transplantation. J Immunol Methods 2006; 311:164-73. [PMID: 16530782 DOI: 10.1016/j.jim.2006.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 12/28/2005] [Accepted: 02/01/2006] [Indexed: 11/28/2022]
Abstract
The detection and quantification of specific T lymphocytes against human cytomegalovirus (HCMV) has proven an important laboratory marker in the monitoring of patients after stem cell transplantation (SCT). In these patients HCMV infections may cause severe disease and death. However, the determination of HCMV-specific T lymphocytes may be limited by lymphopenia occurring after transplantation. We evaluated a commercial test kit for the reliable determination of HCMV-specific T lymphocyte development in lymphopenic patients after stem cell transplantation. Using a whole blood protocol for the flow cytometric detection of antigen-specific CD4(+) T-helper and CD8(+) cytotoxic T lymphocytes this test kit measures intracellular cytokine production after stimulation with HCMV antigen. The measurement of HCMV-specific T lymphocytes was feasible when at least 3,000 CD4(+) or 1,000 CD8(+) T cells could be counted by flow cytometry. Detection of HCMV-specific T lymphocytes was possible, on average, 67 (SD+/-61) days after transplantation for CD4(+) cells and 27 (SD+/-13) days for CD8(+) cells, thus being still within the critical time for HCMV reactivation. In conclusion, the use of modern test kits permits the measurement of HCMV-specific T lymphocytes in stem cell transplant recipients and may be included in the HCMV monitoring system after SCT.
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Affiliation(s)
- Sigune Buxbaum
- Institute for Medical Virology, Johann Wolfgang Goethe University Frankfurt, Paul Ehrlich-Str. 40, 60596 Frankfurt, Germany.
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He XH, Xu LH, Liu Y. Procedure for preparing peptide-major histocompatibility complex tetramers for direct quantification of antigen-specific cytotoxic T lymphocytes. World J Gastroenterol 2005; 11:4180-7. [PMID: 16015686 PMCID: PMC4615439 DOI: 10.3748/wjg.v11.i27.4180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Revised: 11/14/2004] [Accepted: 11/19/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To establish a simplified method for generating peptide-major histocompatibility complex (MHC) class I tetramers. METHODS cDNAs encoding the extracellular domain of human lymphocyte antigen (HLA)-A*0201 heavy chain (A2) and beta(2)-microglobulin (beta(2)m) from total RNA extracted from leukocytes of HLA-A2(+) donors were cloned into separate expression vectors by reverse transcription-polymerase chain reaction. The recombinant A2 and beta(2)m proteins were expressed in Escherichia coli strain BL21(DE3) and recovered from the inclusion body fraction. Soluble A2 proteins loaded with specific antigen peptides were refolded by dilution from the heavy chain in the presence of light chain beta(2)m and HLA-A2-restricted peptide antigens. The refolded A2 monomers were biotinylated with a commercial biotinylation enzyme (BirA) and purified by low pressure anion exchange chromatography on a Q-Sepharose (fast flow) column. The tetramers were then formed by mixing A2 monomers with streptavidin-PE in a molar ratio of 4:1. Flow cytometry was used to confirm the expected tetramer staining of CD8(+) T cells. RESULTS Recombinant genes for HLA-A*0201 heavy chain (A2) fused to a BirA substrate peptide (A2-BSP) and mature beta(2)m from HLA-A2(+) donor leukocytes were successfully cloned and highly expressed in E. coli. Two soluble monomeric A2-peptide complexes were reconstituted from A2-BSP in the presence of beta(2)m and peptides loaded with either human cytomegalovirus pp65(495-503) peptide (NLVPMVATV, NLV; designated as A2-NLV) or influenza virus matrix protein Mp58-66 peptide (GILGFVFTL, GIL; designated as A2-GIL). Refolded A2-NLV or A2-GIL monomers were biotinylated and highly purified by single step anion exchange column chromatography. The tetramers were then formed by mixing the biotinylated A2-NLV or A2-GIL monomers with streptavidin-PE, leading to more than 80% multiplication as revealed by SDS-PAGE under non-reducing, unboiled conditions. Flow cytometry revealed that these tetramers could specifically bind to CD8(+) T cells from a HLA-A2(+) donor, but failed to bind to those from a HLA-A2- donor. CONCLUSION The procedure is simple and efficient for generating peptide-MHC tetramers.
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Affiliation(s)
- Xian-Hui He
- Key Laboratory of Ministry of Education of China for Tissue Transplantation and Immunology, Jinan University, Guangzhou 510632, Guangdong Province, China.
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Bunde T, Kirchner A, Hoffmeister B, Habedank D, Hetzer R, Cherepnev G, Proesch S, Reinke P, Volk HD, Lehmkuhl H, Kern F. Protection from cytomegalovirus after transplantation is correlated with immediate early 1-specific CD8 T cells. ACTA ACUST UNITED AC 2005; 201:1031-6. [PMID: 15795239 PMCID: PMC2213133 DOI: 10.1084/jem.20042384] [Citation(s) in RCA: 297] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
T cells are crucial for the control of cytomegalovirus (CMV) in infected individuals. Although CMV-specific T cells can be quantified by various methods, clear correlates of protection from CMV disease have not been defined. However, responses to the pp65 protein are believed to play an important role. Here, the proportions of interferon γ–producing T cells following ex vivo activation with pools of overlapping peptides representing the pp65 and immediate early (IE)-1 proteins were determined at multiple time points and related to the development of CMV disease in 27 heart and lung transplant recipients. Frequencies of IE-1–specific CD8 T cells above 0.2 and 0.4% at day 0 and 2 wk, respectively, or 0.4% at any time during the first months discriminated patients who did not develop CMV disease from patients at risk, 50–60% of whom developed CMV disease. No similar distinction between risk groups was possible based on pp65-specific CD8 or CD4 T cell responses. Remarkably, CMV disease developed exclusively in patients with a dominant pp65-specific CD8 T cell response. In conclusion, high frequencies of IE-1 but not pp65-specific CD8 T cells correlate with protection from CMV disease. These results have important implications for monitoring T cell responses, adoptive cell therapy, and vaccine design.
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Affiliation(s)
- Torsten Bunde
- Institut für Medizinische Immunologie, Charité, Universitätsmedizin Berlin, Campus Mitte, 10098 Berlin, Germany
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